Geoalkalibacter subterraneus sp. nov., an anaerobic Fe(III)- and Mn(IV)-reducing bacterium from a petroleum reservoir, and emended descriptions of the family Desulfuromonadaceae and the genus Geoalkalibacter

A widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer

Microbial extracellular electron transfer (EET) drives various globally important environmental phenomena and has biotechnology applications. Diverse prokaryotes have been proposed to perform EET via surface-displayed "nanowires" composed of multi-heme cytochromes. However, the mechanism that enables only a few cytochromes to polymerize into nanowires is unclear. Here, we identify a highly conserved omcS-companion (osc) cluster that drives the formation of cytochrome OmcS nanowires in Geobacter sulfurreducens. Through a combination of genetic, biochemical, and biophysical methods, we establish that prolyl isomerase-containing chaperon OscH, channel-like OscEFG, and β-propeller-like OscD are involved in the folding, secretion, and morphology maintenance of OmcS nanowires, respectively. OscH and OscG can interact with OmcS. Furthermore, overexpression of oscG accelerates EET by overproducing nanowires in an ATP-dependent manner. Heme loading splits OscD; ΔoscD accelerates cell growth, bundles nanowires into cables. Our findings establish the mechanism and prevalence of a specialized and modular assembly system for nanowires across phylogenetically diverse species and environments.

Variations in microbial community compositions and processes imposed under contrast geochemical contexts in Sicilian mud volcanoes, Italy

Terrestrial mud volcanoes represent surface features of channels for subsurface methane transport and, therefore, constitute an important source of methane emission from natural environments. How microbial processes regulate methane emissions in terrestrial mud volcanoes has yet to be fully addressed. This study demonstrated the geochemical characteristics and microbial communities of four mud volcano and seep sites in two geological settings of Sicily, Italy. At sites within the accretionary wedge that exhibited higher methane and sulfate concentrations, the communities were dominated by members capable of catalyzing methane and sulfate metabolisms and organic degradation. In particular, both anaerobic and aerobic methanotrophs were abundant and their abundance distribution coincided with the geochemical transition. In contrast, the sites near Mount Etna were characterized by high fluid salinity, CO2, and low methane and sulfate concentrations, with communities consisting of halophilic organic degraders and sulfur metabolizers, along with a minor presence of aerobic methanotrophs. Substantial variations in community composition and geochemistry across spatial and vertical redox gradients suggest that physicochemical contexts imposed by the geology, fluid path, and source characteristics play a vital role in shaping community composition and cycling of methane, sulfur and organic carbon in Sicily mud volcanoes.

Changes in microbial communities during high-rate microbial selenate reduction in an up-flow anaerobic fluidized bed reactor

Biological fluidized bed reactor (FBR) is a promising treatment option for removing selenium oxyanions from wastewater by converting them into elemental selenium. The process can achieve high rates and be efficiently operated at low hydraulic retention times (HRT). However, the effects of HRT on the changes in microbial community in the FBR process have not been previously explored. In this study, dynamic changes of microbial communities both on biofilm carrier and in suspension of a selenate-reducing FBR were explored at various HRTs (0.3-120 h). Based on partial 16S rRNA gene sequencing of the microbial communities, alpha diversity of microbial communities in suspension rather than in the biofilm were impacted by low HRTs (0.3 h-3 h). Members from genera Geobacter, Geoalkalibacter, and Geovibrio were the main selenate-reducing bacteria on carrier throughout the FBR process. Genus Geobacter was dominant in FBR carrier at HRT of 24 h-120 h, whereas Geoalkalibacter and Geovibrio dominated at low HRT of 0.3 h-6 h. Suspended microbial communities detected in the FBR effluent were more sensitive to HRT changes than that in biofilm. "Shock loading" at HRT of 0.3 h had a great impact on microbial community compositions both in the biofilm and effluent. Reactor operation in batch mode and long HRT of 24 h helped recover the community from "shock loading" and improved selenite reduction and ethanol oxidation. Redundancy analysis revealed that HRT, influent pH and selenate loading were key operational parameters impacting both the FBR performance and the composition of microbial communities associated with both the FBR carrier and effluent. Overall, the microbial communities in FBR biofilm flexibly responded to the changes of HRT and showed resilience to the temporary shock loading, enabling efficient selenate removal.

Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE

Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s-1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s-1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.

Characterization of archaeal and bacterial communities thriving in methane-seeping on-land mud volcanoes, Niigata, Japan

Submarine mud volcanoes (MVs) have attracted significant interest in the scientific community for obtaining clues on the subsurface biosphere. On-land MVs, which are much less focused in this context, are equally important, and they may even provide insights also for astrobiology of extraterrestrial mud volcanism. Hereby, we characterized microbial communities of two active methane-seeping on-land MVs, Murono and Kamou, in central Japan. 16S rRNA gene profiling of those sites recovered the dominant archaeal sequences affiliated with methanogens. Anaerobic methanotrophs (ANME), with the subgroups ANME-1b and ANME-3, were recovered only from the Murono site albeit a greatly reduced relative abundance in the community compared to those of typical submarine MVs. The bacterial sequences affiliated to Caldatribacteriota JS1 were recovered from both sites; on the other hand, sulfate-reducing bacteria (SRB) of Desulfobulbaceae was recovered only from the Murono site. The major difference of on-land MVs from submarine MVs is that the high concentrations of sulfate are not always introduced to the subsurface from above. In addition, the XRD analysis of Murono shows the absence of sulfate-, sulfur-related mineral. Therefore, we hypothesize one scenario of ANME-1b and ANME-3 thriving at the depth of the Murono site independently from SRB, which is similar to the situations reported in some other methane-seeping sites with a sulfate-depleted condition. We note that previous investigations speculate that the erupted materials from Murono and Kamou originate from the Miocene marine strata. The fact that SRB (Desulfobulbaceae) capable of associating with ANME-3 was recovered from the Murono site presents an alternative scenario: the old sea-related juvenile water somehow worked as the source of additional sulfur-related components for the SRB-ANME syntrophic consortium forming at a deeper zone of the site. However, the reason for the differences between Murono and Kamou is still unknown, and this requires further investigation.

The influence of anaerobic dechlorination on the aerobic degradation of PCBs in e-waste-contaminated soils in an anaerobic-aerobic two-stage treatment

The combination of microbial reductive dechlorination and aerobic oxidation (RD-AO) process was proposed to be a promising strategy for extensive bioremediation of highly chlorinated polychlorinated biphenyls (PCBs). Nonetheless, experimental evidence on the impact of the RD on subsequent AO in anaerobic-aerobic two-stage treatment remains scarce. The present study applied stable-isotope probing (SIP) to explore the RD-AO mediated degradation of PCBs in an e-waste-contaminated soil. The RD-AO treatment resulted in 37.1 % and 48.2 % degradation of PCB180 and PCB9, respectively, while the PCB9 degradation efficiency decreased compared to the sole AO (81.2 %). The inhibition of PCB aerobic degradation might be caused by the alteration of aerobic bacterial community, which was proved by a higher abundance of anaerobic bacteria and a lower abundance of aerobic bacteria being observed in the aerobic stage of RD-AO. Further evidence was obtained using DNA-SIP that the anaerobic stage altered the PCB degraders' community structures and changed three of the five degraders. There were four lineages (Arenimonas, Steroidobacter, Sulfurifustis, and Thermoanaerobacterales) identified as PCB degraders for the first time. Interestingly, three of them were found in RD-AO microcosm, suggesting that anaerobic-aerobic two-stage treatment can recruit novel bacteria involved in PCBs aerobic degradation. The present study provided novel insight into the synergistic integration of anaerobic and aerobic processes for extensive degradation of highly chlorinated PCBs.

Geoalkalibacter halelectricus SAP-1 sp. nov. possessing extracellular electron transfer and mineral-reducing capabilities from a haloalkaline environment

The extracellular electron transfer (EET)-capable electroactive microorganisms (EAMs) play crucial roles in mineral cycling and interspecies electron transfer in different environments and are used as biocatalysts in microbial electrochemical technologies. Studying EAMs from extreme environments is desired to advance the electromicrobiology discipline, understanding their unique metabolic traits with implications to extreme microbiology, and develop specific bioelectrochemical applications. Here, we present a novel haloalkaliphilic bacterium named Geoalkalibacter halelectricus SAP-1, isolated from a microbial electroactive biofilm enriched from the haloalkaline lake sediments. It is a rod-shaped Gram-negative heterotrophic anaerobe that uses various carbon and energy sources and respires on soluble and insoluble terminal electron acceptors. Besides 16S-rRNA and whole-genome-based phylogeny, the GGDC values of 21.7 %, ANI of 78.5, and 2.77 % genomic DNA GC content difference with the closest validly named species Geoalkalibacter ferrihydriticus (DSM 17813^T ) confirmed its novelty. When grown with the solid-state electrode as the only electron acceptor, it produced 460±23 μA/cm² bioelectrocatalytic current, thereby confirming its electroactivity. Further electrochemical analysis revealed the presence of membrane redox components with high formal potentials, putatively involved in the direct mode of EET. These are distinct from EET components reported for any known electroactive microorganisms, including well-studied Geobacter spp., Shewanella spp. and Desulfuromonas acetexigens. Further the capabilities of G. halelectricus SAP-1 to respire soluble as well insoluble electron acceptors including fumarate, SO₄ ^2- , Fe³⁺ , and Mn⁴⁺ suggests its role in cycling these elements in haloalkaline environments. This article is protected by copyright. All rights reserved.

Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.

Responses of microbial communities and their interactions to ibuprofen in a bio-electrochemical system

Ibuprofen has caused great concerns due to their potential environmental risks. However, their removal efficiency and their effects on microbial interactions in bio-electrochemical system remain unclear. To address these issues, a lab-scale bio-electrochemical reactor integrated with sulfur/iron-mediated autotrophic denitrification (BER-S/IAD) system exposing to 1000 μg L^-1 ibuprofen was operated for about two months. Results revealed that the BER-S/IAD system obtained efficient simultaneous denitrification (98.93%) and phosphorus (82.67%) removal, as well as an excellent ibuprofen removal performance (96.98%). Ibuprofen had no significant impacts on the nitrate (NO₃^--N) removal and the ammonia (NH₄⁺-N) accumulation, but decreased the total nitrogen (TN) and total phosphorus (TP) removal efficiencies. MiSeq sequencing analysis revealed that ibuprofen significantly (P < 0.05) decreased the microbial community diversity and changed their overall structure. Some bacteria related to denitrification and phosphorus removal, such as Pseudomonas and Thiobacillus, decreased significantly (P < 0.05). Moreover, molecular ecological network (MEN) analysis revealed that ibuprofen decreased the network's size and complexity, and enhanced the negative correlations of Proteobacteria and Firmicutes. Besides, ibuprofen decreased the links of some keystone bacteria related to denitrification and phosphorus removal. This research could provide a new dimension for our comprehending of the responses of microbial communities and their interactions to ibuprofen in bio-electrochemical system.

Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains

BACKGROUND

Halotolerant Fe (III) oxide reducers affiliated in the family Desulfuromonadaceae are ubiquitous and drive the carbon, nitrogen, sulfur and metal cycles in marine subsurface sediment. Due to their possible application in bioremediation and bioelectrochemical engineering, some of phylogenetically close Desulfuromonas spp. strains have been isolated through enrichment with crystalline Fe (III) oxide and anode. The strains isolated using electron acceptors with distinct redox potentials may have different abilities, for instance, of extracellular electron transport, surface recognition and colonization. The objective of this study was to identify the different genomic signatures between the crystalline Fe (III) oxide-stimulated strain AOP6 and the anode-stimulated strains WTL and DDH964 by comparative genome analysis.

RESULTS

The AOP6 genome possessed the flagellar biosynthesis gene cluster, as well as diverse and abundant genes involved in chemotaxis sensory systems and c-type cytochromes capable of reduction of electron acceptors with low redox potentials. The WTL and DDH964 genomes lacked the flagellar biosynthesis cluster and exhibited a massive expansion of transposable gene elements that might mediate genome rearrangement, while they were deficient in some of the chemotaxis and cytochrome genes and included the genes for oxygen resistance.

CONCLUSIONS

Our results revealed the genomic signatures distinctive for the ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains. These findings highlighted the different metabolic abilities, such as extracellular electron transfer and environmental stress resistance, of these phylogenetically close bacterial strains, casting light on genome evolution of the subsurface Fe (III) oxide reducers.

Substrate salinity: A critical factor regulating the performance of microbial fuel cells, a review

Substrate salinity is a critical factor influencing microbial fuel cells (MFCs) performance and various studies have suggested that increasing substrate salinity first improves MFC performance. However, a further increase in salinity that exceeds the salinity tolerance of exoelectrogens shows negative effects because of inhibited bacterial activity and increased activation losses. In this review, electricity generation and contaminant removal from saline substrates using MFCs are summarized, and results show different optimal salinities for obtaining maximum performance. Then, electroactive bacteria capable of tolerating saline environments and strategies for improving salinity tolerance are discussed. In addition to ohmic resistance and bacterial activity, membrane resistance and catalyst performance will also be affected by substrate salinity, all of which jointly contribute the final overall MFC performance. Therefore, the combined effect of salinity is analyzed to illustrate how the MFC performance changes with increasing salinity. Finally, the challenges and perspectives of MFCs operated in saline environments are discussed.

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia . Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria . Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria , and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.

Microbial electroactive biofilms dominated by Geoalkalibacter spp. from a highly saline-alkaline environment

Understanding of the extreme microorganisms that possess extracellular electron transfer (EET) capabilities is pivotal to advance electromicrobiology discipline and to develop niche-specific microbial electrochemistry-driven biotechnologies. Here, we report on the microbial electroactive biofilms (EABs) possessing the outward EET capabilities from a haloalkaline environment of the Lonar lake. We used the electrochemical cultivation approach to enrich haloalkaliphilic EABs under 9.5 pH and 20 g/L salinity conditions. The electrodes controlled at 0.2 V vs. Ag/AgCl yielded the best-performing biofilms in terms of maximum bioelectrocatalytic current densities of 548 ± 23 and 437 ± 17 µA/cm² with acetate and lactate substrates, respectively. Electrochemical characterization of biofilms revealed the presence of two putative redox-active moieties with the mean formal potentials of 0.183 and 0.333 V vs. Ag/AgCl, which represent the highest values reported to date for the EABs. 16S-rRNA amplicon sequencing of EABs revealed the dominance of unknown Geoalkalibacter sp. at ~80% abundance. Further investigations on the haloalkaliphilic EABs possessing EET components with high formal potentials might offer interesting research prospects in electromicrobiology.

Complete Genome Sequence of Desulfuromonas sp. Strain AOP6, an Iron(III) Reducer Isolated from Subseafloor Sediment

Desulfuromonas sp. strain AOP6, with iron(III)-reducing activity, was isolated from subseafloor sediment in Nankai Trough. We report the complete genome of this strain determined by Illumina MiSeq sequencing and PCR/Sanger sequencing-based gap closing. The genome includes the genes encoding c-type cytochromes, type IV pili, and fatty acid degradation enzymes.

Desulfuromonas sp. strain AOP6, with iron(III)-reducing activity, was isolated from subseafloor sediment in Nankai Trough. We report the complete genome of this strain determined by Illumina MiSeq sequencing and PCR/Sanger sequencing-based gap closing. The genome includes the genes encoding c-type cytochromes, type IV pili, and fatty acid degradation enzymes.

Identification of Persistent Sulfidogenic Bacteria in Shale Gas Produced Waters

Produced waters from hydraulically fractured shale formations give insight into the microbial ecology and biogeochemical conditions down-well. This study explores the potential for sulfide production by persistent microorganisms recovered from produced water samples collected from the Marcellus shale formation. Hydrogen sulfide is highly toxic and corrosive, and can lead to the formation of “sour gas” which is costly to refine. Furthermore, microbial colonization of hydraulically fractured shale could result in formation plugging and a reduction in well productivity. It is vital to assess the potential for sulfide production in persistent microbial taxa, especially when considering the trend of reusing produced waters as input fluids, potentially enriching for problematic microorganisms. Using most probable number (MPN) counts and 16S rRNA gene sequencing, multiple viable strains of bacteria were identified from stored produced waters, mostly belonging to the Genus Halanaerobium, that were capable of growth via fermentation, and produced sulfide when supplied with thiosulfate. No sulfate-reducing bacteria (SRB) were detected through culturing, despite the detection of relatively low numbers of sulfate-reducing lineages by high-throughput 16S rRNA gene sequencing. These results demonstrate that sulfidogenic produced water populations remain viable for years post production and, if left unchecked, have the potential to lead to natural gas souring during shale gas extraction.

Enhancement of COD removal in constructed wetlands treating saline wastewater: Intertidal wetland sediment as a novel inoculation

This study investigated intertidal wetland sediment (IWS) as a novel inoculation source for saline wastewater treatment in constructed wetlands (CWs). Samples of IWS (5-20 cm subsurface sediment), which are highly productive and rich in halophilic and anaerobic bacteria, were collected from a high-salinity natural wetland and added to CW matrix. IWS-supplemented CW microcosms that are planted and unplanted Phragmites australis were investigated under salty (150 mM NaCl: PA+(S) and CT+(S)) and non-salty (0 mM NaCl: PA+ and CT+) conditions. The chemical oxygen demand (COD) removal potential of IWS-supplemented CWs was compared with that of conventional CWs without IWS (PA(S) and CT(S), PA, and CT). Results showed that the COD removal rate was higher in PA+(S) (51.80% ± 3.03%) and CT+(S) (29.20% ± 1.26%) than in PA(S) (27.40% ± 3.09%) and CT(S) (27.20% ± 3.06%) at 150 mM NaCl. The plants' chlorophyll content and antioxidant enzyme activity indicated that the addition of IWS enhanced the resistance of plants to salt. Microbial community analysis showed that the dominant microorganisms in PA+(S) and CT+(S), namely, Anaerolineae, Desulfobacterales, and Desulfuromonadales, enhanced the organic removal rates via anaerobic degradation. IWS-induced Dehalococcoides, which is a key participant in ethylene formation, improved the plants' stress tolerance. Several halophilic/tolerant microorganisms were also detected in the CW system with IWS. Thus, IWS is a promising inoculation source for CWs that treat saline wastewater.

Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov

In paddy soil, bacteria from the family Geobacteraceae have been shown to strongly contribute to the biogeochemical cycle. However, no Geobacteraceae species with validly published names have been isolated from paddy soil. In this study, we isolated and characterized four novel ferric reducing bacteria in the family Geobacteraceae from the paddy soils of three different fields in Japan. The four strains, S43T, Red53T, S62T, and Red111T, were Gram-stain negative, strictly anaerobic, chemoheterotrophic, and motile with peritrichous flagella. Phylogenetic studies based on 16S rRNA gene sequences, five concatenated housekeeping genes (fusA, rpoB, recA, nifD, and gyrB) and 92 concatenated core genes revealed that the four strains belong to the family Geobacteraceae and are most closely related to Geobacter bemidjiensis BemT (97.4-98.2%, 16S rRNA gene sequence similarities) and Geobacter bremensis Dfr1T (97.1-98.0%). Genomic analysis with average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) calculations clearly distinguished the four isolated strains from other species of the family Geobacteraceae and indicated that strains S43T, Red53T, S62T, and Red111T represent independent species, with values below the thresholds for species delineation. Chemotaxonomic characteristics, including major fatty acid and whole cell protein profiles, showed differences among the isolates and their closest relatives, which were consistent with the results of DNA fingerprints and physiological characterization. Additionally, each of the four isolates shared a low 16S rRNA gene sequence similarity (92.4%) and average amino acid identity (AAI) with the type strain of the type species Geobacter metallireducens. Overall, strains S43T, Red53T, S62T, and Red111T represent four novel species, which we propose to classify in a novel genus of the family Geobacteraceae, and the names Geomonas oryzae gen. nov., sp. nov. (type strain S43T), Geomonas edaphica sp. nov. (type strain Red53T), Geomonas ferrireducens sp. nov. (type strain S62T), and Geomonas terrae sp. nov. (type strain Red111T) are proposed. Based on phylogenetic and genomic analyses, we also propose the reclassification of Geobacter bremensis as Geomonas bremensis comb. nov., Geobacter pelophilus as Geomonas pelophila comb. nov., and Geobacter bemidjiensis as Geomonas bemidjiensis comb. nov.

The mutual influence between corrosion and the surrounding soil microbial communities of buried petroleum pipelines

Buried petroleum pipeline corrosion and leaks cause inevitable changes in the microbial communities of the surrounding soils. In addition, soils with different microbial communities can make different contributions to buried pipeline corrosion. Three kinds of soil samples of buried petroleum pipelines under different corrosion and petroleum contamination conditions were collected from the Shengli Oilfield of China to investigate the mutual influence between corrosion and the microbial communities of the surrounding soil. The 16S rRNA gene high-throughput Illumina MiSeq sequencing was used to analyze the microbial communities of different surrounding soils. Electrochemical tests were performed for steel corrosion investigation. The results showed that the microbial diversity of the surrounding soils of corroded pipelines with/without petroleum contamination (O-soil and C-soil, respectively) decreased significantly as compared with that of the non-corroded and non-contaminated ones (NC-soil). The C-soil contained more abundant Balneolaceae (Balneola, KSA1), Flavobacteriaceae (Muricauda, Gramella) and Desulfuromonadaceae (Pelobacter, Geoalkalibacter). The O-soil possessed a greater abundance of Halomonas, Pseudoalteromonas, Psychrobacter and Dietzia, which were reported to have a capacity for hydrocarbon degradation. Moreover, electrochemical measurements indicated that the microcosm of the C-soil and NC-soil promoted steel corrosion, while the C-soil community showed a slightly higher corrosion rate. However, the O-soil community mitigated the steel corrosion. These observations suggested that pipeline corrosion increased proportions of microorganisms, which are likely related to fermentation, sulfur respiration, iron respiration and manganese respiration in surrounding soils and enhanced the soil corrosivity, while petroleum contamination weakened the corrosion ability and promoted the growth of hydrocarbon-degrading organisms in the microbial community.

Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico

Marine sediments are an example of one of the most complex microbial habitats. These bacterial communities play an important role in several biogeochemical cycles in the marine ecosystem. In particular, the Gulf of Mexico has a ubiquitous concentration of hydrocarbons in its sediments, representing a very interesting niche to explore. Additionally, the Mexican government has opened its oil industry, offering several exploration and production blocks in shallow and deep water in the southwestern Gulf of Mexico (swGoM), from which there are no public results of conducted studies. Given the higher risk of large-scale oil spills, the design of contingency plans and mitigation activities before oil exploitation is of growing concern. Therefore, a bacterial taxonomic baseline profile is crucial to understanding the impact of any eventual oil spill. Here, we show a genus level taxonomic profile to elucidate the bacterial baseline, pointing out richness and relative abundance, as well as relationships with 79 abiotic parameters, in an area encompassing ∼150,000 km2, including a region where the exploitation of new oil wells has already been authorized. Our results describe for the first time the bacterial landscape of the swGoM, establishing a bacterial baseline "core" of 450 genera for marine sediments in this region. We can also differentiate bacterial populations from shallow and deep zones of the swGoM based on their community structure. Shallow sediments have been chronically exposed to aromatic hydrocarbons, unlike deep zones. Our results reveal that the bacterial community structure is particularly enriched with hydrocarbon-degrading bacteria in the shallow zone, where a greater aromatic hydrocarbon concentration was determined. Differences in the bacterial communities in the swGoM were also observed through a comprehensive comparative analysis relative to various marine sediment sequencing projects, including sampled sites from the Deep Water Horizon oil spill. This study in the swGoM provides clues to the bacterial population adaptation to the ubiquitous presence of hydrocarbons and reveals organisms such as Thioprofundum bacteria with potential applications in ecological surveillance. This resource will allow us to differentiate between natural conditions and alterations generated by oil extraction activities, which, in turn, enables us to assess the environmental impact of such activities.

Microbial Mineralization of Montmorillonite in Low-Permeability Oil Reservoirs for Microbial Enhanced Oil Recovery

Microbial mineralization (corrosion, decomposition, and weathering) has been investigated for its role in the extraction and recovery of metals from ores. Here we report our application of biomineralization for the microbial enhanced oil recovery in low-permeability oil reservoirs. It aimed to reveal the etching mechanism of the four Fe(III)-reducing microbial strains under anaerobic growth conditions on Ca-montmorillonite. The mineralogical characterization of Ca-montmorillonite was performed by Fourier transform infrared spectroscopy, X-ray powder diffraction, scanning electron microscopy, and energy-dispersive spectrometry. Results showed that the microbial strains could efficiently reduce Fe(III) at an optimal rate of 71%, alter the crystal lattice structure of the lamella to promote interlayer cation exchange, and efficiently inhibit Ca-montmorillonite swelling at a rate of 48.9%.IMPORTANCE Microbial mineralization is ubiquitous in the natural environment. Microbes in low-permeability reservoirs are able to facilitate alteration of the structure and phase of the Fe-poor minerals by reducing Fe(III) and inhibiting clay swelling, which is still poorly studied. This study aimed to reveal the interaction mechanism between Fe(III)-reducing bacterial strains and Ca-montmorillonite under anaerobic conditions and to investigate the extent and rates of Fe(III) reduction and phase changes with their activities. Application of Fe(III)-reducing bacteria will provide a new way to inhibit clay swelling, to elevate reservoir permeability, and to reduce pore throat resistance after water flooding for enhanced oil recovery in low-permeability reservoirs.

Effect of long term application of tetrakis(hydroxymethyl)phosphonium sulfate (THPS) in a light oil-producing oilfield

Samples of (I) produced waters, (II) central processing facility (CPF) waters and (III) pipeline solids were collected from a light oil-producing field. The biocide, tetrakis(hydroxymethyl)phosphonium sulfate (THPS) was routinely used in the CPF. Samples monitoring indicated that THPS was effective in microbial control but also increased concentrations of sulfate and phosphate in transitioning from Type I to Type II waters. Type II waters had high concentrations (up to 60 mM) of acetate but low most probable numbers (MPNs) of acid-producing and sulfate-reducing bacteria, indicating the presence of active biocide, as high MPNs were found in Type I waters. Solids had high phosphate and high MPNs, indicating that THPS was inactive. Solids had oil and an anaerobic community dominated by Acetobacterium, which may contribute to conversion of oil to acetate. The presence of THPS prevented the use of this acetate in Type II waters, where it accumulated to unusually high concentrations.

Microbial fuel cells in saline and hypersaline environments: Advancements, challenges and future perspectives

This review is aimed to report the possibility to utilize microbial fuel cells for the treatment of saline and hypersaline solutions. An introduction to the issues related with the biological treatment of saline and hypersaline wastewater is reported, discussing the limitation that characterizes classical aerobic and anaerobic digestions. The microbial fuel cell (MFC) technology, and the possibility to be applied in the presence of high salinity, is discussed before reviewing the most recent advancements in the development of MFCs operating in saline and hypersaline conditions, with their different and interesting applications. Specifically, the research performed in the last 5years will be the main focus of this review. Finally, the future perspectives for this technology, together with the most urgent research needs, are presented.

Microbial Community Composition and Functional Capacity in a Terrestrial Ferruginous, Sulfate-Depleted Mud Volcano

Terrestrial mud volcanoes (MVs) are an important natural source of methane emission. The role of microbial processes in methane cycling and organic transformation in such environments remains largely unexplored. In this study, we aim to uncover functional potentials and community assemblages across geochemical transitions in a ferruginous, sulfate-depleted MV of eastern Taiwan. Geochemical profiles combined with 16S rRNA gene abundances indicated that anaerobic oxidation of methane (AOM) mediated by ANME-2a group coincided with iron/manganese reduction by Desulfuromonadales at shallow depths deprived of sulfate. The activity of AOM was stimulated either by methane alone or by methane and a range of electron acceptors, such as sulfate, ferrihydrite, and artificial humic acid. Metagenomic analyses revealed that functional genes for AOM and metal reduction were more abundant at shallow intervals. In particular, genes encoding pili expression and electron transport through multi-heme cytochromes were prevalent, suggesting potential intercellular interactions for electron transport involved in AOM. For comparison, genes responsible for methanogenesis and degradation of chitin and plant-derived molecules were more abundant at depth. The gene distribution combined with the enhanced proportions of 16S rRNA genes related to methanogens and heterotrophs, and geochemical characteristics suggest that particulate organic matter was degraded into various organic entities that could further fuel in situ methanogenesis. Finally, genes responsible for aerobic methane oxidation were more abundant in the bubbling pool and near-surface sediments. These methane oxidizers account for the ultimate attenuation of methane discharge into the atmosphere. Overall, our results demonstrated that various community members were compartmentalized into stratified niches along geochemical gradients. These community members form a metabolic network that cascades the carbon transformation from the upstream degradation of recalcitrant organic carbon with fermentative production of labile organic entities and methane to downstream methane oxidation and metal reduction near the surface. Such a metabolic architecture enables effective methane removal under ferruginous, sulfate-depleted conditions in terrestrial MVs.

Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite

Microbial communities in shale oil fields are still poorly known. We obtained samples of injection, produced and facility waters from a Bakken shale oil field in Saskatchewan, Canada with a resident temperature of 60°C. The injection water had a lower salinity (0.7 Meq of NaCl) than produced or facility waters (0.6-3.6 Meq of NaCl). Salinities of the latter decreased with time, likely due to injection of low salinity water, which had 15-30 mM sulfate. Batch cultures of field samples showed sulfate-reducing and nitrate-reducing bacteria activities at different salinities (0, 0.5, 0.75, 1.0, 1.5, and 2.5 M NaCl). Notably, at high salinity nitrite accumulated, which was not observed at low salinity, indicating potential for nitrate-mediated souring control at high salinity. Continuous culture chemostats were established in media with volatile fatty acids (a mixture of acetate, propionate and butyrate) or lactate as electron donor and nitrate or sulfate as electron acceptor at 0.5 to 2.5 M NaCl. Microbial community analyses of these cultures indicated high proportions of Halanaerobium, Desulfovermiculus, Halomonas, and Marinobacter in cultures at 2.5 M NaCl, whereas Desulfovibrio, Geoalkalibacter, and Dethiosulfatibacter were dominant at 0.5 M NaCl. Use of bioreactors to study the effect of nitrate injection on sulfate reduction showed that accumulation of nitrite inhibited SRB activity at 2.5 M but not at 0.5 M NaCl. High proportions of Halanaerobium and Desulfovermiculus were found at 2.5 M NaCl in the absence of nitrate, whereas high proportions of Halomonas and no SRB were found in the presence of nitrate. A diverse microbial community dominated by the SRB Desulfovibrio was observed at 0.5 M NaCl both in the presence and absence of nitrate. Our results suggest that nitrate injection can prevent souring provided that the salinity is maintained at a high level. Thus, reinjection of high salinity produced water amended with nitrate maybe be a cost effective method for souring control.

Performance of CSTR-EGSB-SBR system for treating sulfate-rich cellulosic ethanol wastewater and microbial community analysis

Performance and microbial community composition were evaluated in a two-phase anaerobic and aerobic system treating sulfate-rich cellulosic ethanol wastewater (CEW). The system was operated at five different chemical oxygen demand (COD)/SO₄^2- ratios (63.8, 26.3, 17.8, 13.7, and 10.7). Stable performance was obtained for total COD removal efficiency (94.5%), sulfate removal (89.3%), and methane production rate (11.5 L/day) at an organic loading rate of 32.4 kg COD/(m³·day). The acidogenic reactor made a positive contribution to net VFAs production (2318.1 mg/L) and sulfate removal (60.9%). Acidogenic bacteria (Megasphaera, Parabacteroides, unclassified Ruminococcaceae spp., and Prevotella) and sulfate-reducing bacteria (Butyrivibrio, Megasphaera) were rich in the acidogenic reactor. In the methanogenic reactor, high diversity of microorganisms corresponded with a COD removal contribution of 83.2%. Moreover, methanogens (Methanosaeta) were predominant, suggesting that these organisms played an important role in the acetotrophic methanogenesis pathway. The dominant aerobic bacteria (Truepera) appeared to have been responsible for the COD removal of the SBR. These results indicate that dividing the sulfate reduction process could effectively minimize sulfide toxicity, which is important for the successful operation of system treating sulfate-rich CEW.

Enhancing biomethanogenic treatment of fresh incineration leachate using single chambered microbial electrolysis cells

Methanogenic treatment of municipal solid waste (MSW) incineration leachate can be hindered by high concentrations of refractory organic matter and humification of compounds in the leachate. In an attempt to overcome some of these impediments, microbial electrolysis cells (MECs) were incorporated into anaerobic digesters (ADMECs). COD removal efficiencies and methane production were 8.7% and 44.3% higher in ADMECs than in controls, and ADMEC reactors recovered more readily from souring caused by high organic loading rates. The degradation rate of large macromolecules was substantially higher (96% vs 81%) in ADMEC than control effluent, suggesting that MECs stimulated degradation of refractory organic matter and reduced humification. Exoelectrogenic bacteria and microorganisms known to form syntrophic partnerships were enriched in ADMECs. These results show that ADMECs were more effective at treatment of MSW incineration leachate, and should be taken into consideration when designing future treatment facilities.

Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils

The possibility that Methanothrix (formerly Methanosaeta) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated with Geobacter species, but sequences most closely related to putative e-pilin genes from genera such as Desulfobacterium, Deferribacter, Geoalkalibacter, and Desulfobacula, were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered with Geobacter species, and the finding that Geobacter spp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribed Geobacter genes. In addition, homologs of genes encoding OmcS, a c-type cytochrome associated with the e-pili of G. sulfurreducens and required for DIET, were also highly expressed in the soils. Methanothrix species in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO₂ reduction in Methanothrix Thus, these results are consistent with a model in which Geobacter species were providing electrons to Methanothrix species for methane production through electrical connections of e-pili.IMPORTANCEMethanothrix species are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons for Methanothrix in methanogenic rice paddy soils is important because it demonstrates that the contribution that Methanothrix makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when Methanothrix species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus, Methanothrix growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that Geobacter species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with Methanothrix spp., and possibly other methanogens, via DIET.

Assessment of the performance of SMFCs in the bioremediation of PAHs in contaminated marine sediments under different redox conditions and analysis of the associated microbial communities

The biodegradation of naphthalene, 2-methylnaphthalene and phenanthrene was evaluated in marine sediment microbial fuel cells (SMFCs) under different biodegradation conditions, including sulfate reduction as a major biodegradation pathway, employment of anode as terminal electron acceptor (TEA) under inhibited sulfate reducing bacteria activity, and combined sulfate and anode usage as electron acceptors. A significant removal of naphthalene and 2-methylnaphthalene was observed at early stages of incubation in all treatments and was attributed to their high volatility. In the case of phenanthrene, a significant removal (93.83±1.68%) was measured in the closed circuit SMFCs with the anode acting as the main TEA and under combined anode and sulfate reduction conditions (88.51±1.3%). A much lower removal (40.37±3.24%) was achieved in the open circuit SMFCs operating with sulfate reduction as a major biodegradation pathway. Analysis of the anodic bacterial community using 16S rRNA gene pyrosequencing revealed the enrichment of genera with potential exoelectrogenic capability, namely Geoalkalibacter and Desulfuromonas, on the anode of the closed circuit SMFCs under inhibited SRB activity, while they were not detected on the anode of open circuit SMFCs. These results demonstrate the role of the anode in enhancing PAHs biodegradation in contaminated marine sediments and suggest a higher system efficiency in the absence of competition between microbial redox processes (under SRB inhibition), namely due to the anode enrichment with exoelectrogenic bacteria, which is a more energetically favorable mechanism for PAHs oxidation than sulfate.

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H₂ as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe₂O₃). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe₃(PO₄)₂] and siderite (FeCO₃). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov.

IMPORTANCE

A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.

Isolation and Genomic Characterization of 'Desulfuromonas soudanensis WTL', a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine

Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, ‘Desulfuromonas soudanensis’ strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that ‘D. soudanensis’ releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. ‘D. soudanensis’ contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of ‘D. soudanensis’ underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.

Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria

Exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 pH) mid-temperature (55-85°C) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. To gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of Gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media with 50 μg ml(-1) vancomycin. Surprisingly, this Gram-positive-specific antibiotic eliminated the entire culturable-diversity of chemoorganotrophic and sulfur-chemolithotrophic bacteria present in the tested hot water inocula. Moreover, it also killed all the Gram-negative hot-spring isolates that were obtained in vancomycin-free media. Concurrent literature search for the description of Gram-negative thermophilic bacteria revealed that at least 16 of them were reportedly vancomycin-susceptible. While these data suggested that vancomycin-susceptibility could be a global trait of thermophilic bacteria (irrespective of their taxonomy, biogeography and Gram-character), MALDI Mass Spectroscopy of the peptidoglycans of a few Gram-negative thermophilic bacteria revealed that tandem alanines were present in the fourth and fifth positions of their muropeptide precursors (MPPs). Subsequent phylogenetic analyses revealed a close affinity between the D-alanine-D-alanine ligases (Ddl) of taxonomically-diverse Gram-negative thermophiles and the thermostable Ddl protein of Thermotoga maritima, which is well-known for its high specificity for alanine over other amino acids. The Ddl tree further illustrated a divergence between the homologs of Gram-negative thermophiles and mesophiles, which broadly coincided with vancomycin-susceptibility and vancomycin-resistance respectively. It was thus hypothesized that thermophilic Ddls have been evolutionarily selected to favor a D-ala-D-ala bonding. However, preference for D-ala-D-ala-terminated MPPs does not singlehandedly guarantee vancomycin susceptibility of thermophilic bacteria as the large and relatively-hydrophilic vancomycin molecule has to cross the outer membrane before it can inhibit peptidoglycan biosynthesis. Literature shows that many mesophilic Gram-negative bacteria also have D-ala-D-ala-terminated MPPs, but they still remain resistant to vancomycin due to the relative impermeability of their membranes. But the global vancomycin-susceptibility phenotype of thermophilic bacteria itself testifies that the drug crosses the membrane in all these cases. As a corollary, it seems quite likely that the outer membranes of thermophilic bacteria have some yet-unknown characteristic feature(s) that invariably ensures the entry of vancomycin.

Anode Biofilms of Geoalkalibacter ferrihydriticus Exhibit Electrochemical Signatures of Multiple Electron Transport Pathways

Thriving under alkaliphilic conditions, Geoalkalibacter ferrihydriticus (Glk. ferrihydriticus) provides new applications in treating alkaline waste streams as well as a possible new model organism for microbial electrochemistry. We investigated the electrochemical response of biofilms of the alkaliphilic anode-respiring bacterium (ARB) Glk. ferrihydriticus voltammetry (CV), electrochemical impedance spectroscopy (EIS), and chronoamperometry. We observed there to be at least four dominant electron transfer pathways, with their contribution to the overall current produced dependent on the set anode potential. These pathways appear to be manifested at midpoint potentials of approximately -0.14 V, -0.2 V, -0.24 V, and -0.27 V vs standard hydrogen electrode. The individual contributions of the pathways change upon equilibration from a set anode potential to another anode potential. Additionally, the contribution of each pathway to the overall current produced is reversible when the anode potential is changed back to the original set potential. The pathways involved in anode respiration in Glk. ferrihydriticus biofilms follow a similar, but more complicated, pattern as compared to those in the model ARB, Geobacter sulfurreducens. This greater diversity of electron transport pathways in Glk. ferrihydriticus could be related to its wider metabolic capability (e.g., higher pH and larger set of possible substrates, among others).

Microbial characterization of anode-respiring bacteria within biofilms developed from cultures previously enriched in dissimilatory metal-reducing bacteria

This work evaluated the use of a culture enriched in DMRB as a strategy to enrich ARB on anodes. DMRB were enriched with Fe(III) as final electron acceptor and then transferred to a potentiostatically-controlled system with an anode as sole final electron acceptor. Three successive iron-enrichment cultures were carried out. The first step of enrichment revealed a successful selection of the high current-producing ARB Geoalkalibacter subterraneus. After few successive enrichment steps, the microbial community analysis in electroactive biofilms showed a significant divergence with an impact on the biofilm electroactivity. Enrichment of ARB in electroactive biofilms through the pre-selection of DMRB should therefore be carefully considered.

Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria

We sequenced and annotated genomes of two haloalkaliphilic Deltaproteobacteria, Geoalkalibacter ferrihydriticus Z-0531^T (DSM 17813) and Geoalkalibacter subterraneus Red1^T (DSM 23483). During assembly, we discovered that the DSMZ stock culture of G. subterraneus was contaminated. We reisolated G. subterraneus in axenic culture and redeposited it in DSMZ and JCM.

Bacterial diversity in relatively pristine and anthropogenically-influenced mangrove ecosystems (Goa, India)

To appreciate differences in benthic bacterial community composition at the relatively pristine Tuvem and the anthropogenically-influenced Divar mangrove ecosystems in Goa, India, parallel tag sequencing of the V6 region of 16S rDNA was carried out. We hypothesize that availability of extraneously-derived anthropogenic substrates could act as a stimulatant but not a deterrent to promote higher bacterial diversity at Divar. Our observations revealed that the phylum Proteobacteria was dominant at both locations comprising 43–46% of total tags. The Tuvem ecosystem was characterized by an abundance of members belonging to the class Deltaproteobacteria (21%), ~ 2100 phylotypes and 1561 operational taxonomic units (OTUs) sharing > 97% similarity. At Divar, the Gammaproteobacteria were ~ 2× higher (17%) than at Tuvem. A more diverse bacterial community with > 3300 phylotypes and > 2000 OTUs mostly belonging to Gammaproteobacteria and a significantly higher DNT (n = 9, p < 0.001, df = 1) were recorded at Divar. These findings suggest that the quantity and quality of pollutants at Divar are perhaps still at a level to maintain high diversity. Using this technique we could show higher diversity at Divar with the possibility of Gammaproteobacteria contributing to modulating excess nitrate.

Facultative nitrate reduction by electrode-respiring Geobacter metallireducens biofilms as a competitive reaction to electrode reduction in a bioelectrochemical system

Alternative metabolic options of exoelectrogenic biofilms in bioelectrochemical systems (BESs) are important not only to explain the fundamental ecology and performance of these systems but also to develop reliable integrated nutrient removal strategies in BESs, which potentially involve substrates or intermediates that support/induce those alternative metabolisms. This research focused on dissimilatory nitrate reduction as an alternative metabolism to dissimilatory anode reduction. Using the exoelectrogenic nitrate reducer Geobacter metallireducens, the critical conditions controlling those alternative metabolisms were investigated in two-chamber, potentiostatically controlled BESs at various anode potentials and biofilm thicknesses and challenged over a range of nitrate concentrations. Results showed that anode-reducing biofilms facultatively reduced nitrate at all tested anode potentials (-150 to +900 mV vs Standard Hydrogen Electrode) with a rapid metabolic shift. The critical nitrate concentration that triggered a significant decrease in BES performance was a function of anode biofilm thickness but not anode potential. This indicates that these alternative metabolisms were controlled by the availability of nitrate, which is a function of nitrate concentration in bulk solution and its diffusion into an anode-reducing biofilm. Coulombic recovery decreased as a function of nitrate dose due to electron-acceptor substrate competition, and nitrate-induced suspended biomass growth decreased the effluent quality.

Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs

The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO₂, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed.

Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells

The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S., but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina MiSeq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producing wells. In addition, the well waters were incubated with a suite of fermentative and methanogenic substrates in an effort to stimulate microbial methane generation. The three wells exhibited substantial differences in their community structure that may arise from their different drilling and fracturing histories. Bacterial sequences greatly outnumbered those of archaea and shared highest similarity to previously described cultures of mesophiles and moderate halophiles within the Firmicutes, Bacteroidetes, and δ- and ε-Proteobacteria. The majority of archaeal sequences shared highest sequence similarity to uncultured euryarchaeotal environmental clones. Some sequences closely related to cultured methylotrophic and hydrogenotrophic methanogens were also present in the initial well water. Incubation with methanol and trimethylamine stimulated methylotrophic methanogens and resulted in the largest increase in methane production in the formation waters, while fermentation triggered by the addition of yeast extract and formate indirectly stimulated hydrogenotrophic methanogens. The addition of sterile powdered shale as a complex natural substrate stimulated the rate of methane production without affecting total methane yields. Depletion of methane indicative of anaerobic methane oxidation (AMO) was observed over the course of incubation with some substrates. This process could constitute a substantial loss of methane in the shale formation.

Generation of high current densities by pure cultures of anode-respiring Geoalkalibacter spp. under alkaline and saline conditions in microbial electrochemical cells

Anode-respiring bacteria (ARB) generate electric current in microbial electrochemical cells (MXCs) by channeling electrons from the oxidation of organic substrates to an electrode. Production of high current densities by monocultures in MXCs has resulted almost exclusively from the activity of Geobacter sulfurreducens, a neutrophilic freshwater Fe(III)-reducing bacterium and the highest-current-producing member documented for the Geobacteraceae family of the Deltaproteobacteria. Here we report high current densities generated by haloalkaliphilic Geoalkalibacter spp., thus broadening the capability for high anode respiration rates by including other genera within the Geobacteraceae. In this study, acetate-fed pure cultures of two related Geoalkalibacter spp. produced current densities of 5.0 to 8.3 and 2.4 to 3.3 A m⁻² under alkaline (pH 9.3) and saline (1.7% NaCl) conditions, respectively. Chronoamperometric studies of halophilic Glk. subterraneus DSM 23483 and alkaliphilic Glk. ferrihydriticus DSM 17813 suggested that cells performed long-range electron transfer through electrode-attached biofilms and not through soluble electron shuttles. Glk. ferrihydriticus also oxidized ethanol directly to produce current, with maximum current densities of 5.7 to 7.1 A m⁻² and coulombic efficiencies of 84 to 95%. Cyclic voltammetry (CV) elicited a sigmoidal response with characteristic onset, midpoint, and saturation potentials, while CV performed in the absence of an electron donor suggested the involvement of redox molecules in the biofilm that were limited by diffusion. These results matched those previously reported for actively respiring Gb. sulfurreducens biofilms producing similar current densities (~5 to 9 A m⁻²).

This study establishes the highest current densities ever achieved by pure cultures of anode-respiring bacteria (ARB) under alkaline and saline conditions in microbial electrochemical cells (MXCs) and provides the first electrochemical characterization of the genus Geoalkalibacter. Production of high current densities among the Geobacteraceae is no longer exclusive to Geobacter sulfurreducens, suggesting greater versatility for this family in fundamental and applied microbial electrochemical cell (MXC) research than previously considered. Additionally, this work raises the possibility that different members of the Geobacteraceae have conserved molecular mechanisms governing respiratory extracellular electron transfer to electrodes. Thus, the capacity for high current generation may exist in other uncultivated members of this family. Advancement of MXC technology for practical uses must rely on an expanded suite of ARB capable of using different electron donors and producing high current densities under various conditions. Geoalkalibacter spp. can potentially broaden the practical capabilities of MXCs to include energy generation and waste treatment under expanded ranges of salinity and pH.

Enrichment and analysis of anode-respiring bacteria from diverse anaerobic inocula

One of the limitations currently faced by microbial electrochemical cell (MXC) technologies lies in the shortage of different organisms capable of forming a biofilm and channeling electrons from substrates to the anode at high current densities. Using a poised anode (-0.30 V vs Ag/AgCl) and acetate as the electron donor in a MXC, we demonstrated the presence of highly efficient anode-respiring bacteria (ARB) able to produce high current densities (>1.5 A/m(2) anode) in seven out of thirteen environmental samples. These included marshes, lake sediments, saline microbial mats, and anaerobic soils obtained from geographically diverse locations. Our microbial ecology analysis, using pyrosequencing, shows that bacteria related to the genus Geobacter, a known and commonly found ARB, dominate only two of the biofilm communities producing high current; other biofilm communities contained different known and/or novel ARB. The presence of ARB in geographically diverse locations indicates that ARB thrive in a wide range of ecosystems. Studying ARB from different environmental conditions will allow us to better understand the ubiquity of anode respiration, compare the capabilities of different ARB consortia, and find ARB with useful metabolic capacities for future applications.

Deferrisoma camini gen. nov., sp. nov., a moderately thermophilic, dissimilatory iron(III)-reducing bacterium from a deep-sea hydrothermal vent that forms a distinct phylogenetic branch in the Deltaproteobacteria

A moderately thermophilic, anaerobic, dissimilatory iron(III)-reducing bacterium (strain S3R1(T)) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the Pacific Ocean at a depth of about 2150 m. Cells of strain S3R1(T) were ovals to short rods with a single polar flagellum, Gram-stain-negative, 0.5-0.6 µm in diameter and 0.8-1.3 µm long, growing singly or in pairs. The temperature range for growth was 36-62 °C, with an optimum at 50 °C. The pH range for growth was 5.5-7.5, with an optimum at pH 6.5. Growth of strain S3R1(T) was observed at NaCl concentrations ranging from 1.0 to 5.0 % (w/v), with an optimum at 2.0-2.5 % (w/v). The isolate used acetate, fumarate, malate, maleinate, succinate, propanol, palmitate, stearate, peptone and yeast extract as electron donors for growth and iron(III) reduction. All electron donors were oxidized completely to CO(2) and H(2)O. Iron(III) (in the form of ferrihydrite, ferric citrate or ferric nitrilotriacetate) and elemental sulfur (S(0)) were the electron acceptors that supported growth. The DNA G+C content was 64.4 mol%. Results of 16S rRNA gene sequence analysis showed that the novel bacterium was related to representatives of the orders Desulfuromonadales and Syntrophobacterales with 84-86 % sequence similarity and formed a distinct phylogenetic branch in the Deltaproteobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the new isolate represents the sole species of a novel genus, Deferrisoma camini gen. nov., sp. nov. The type strain of Deferrisoma camini is S3R1(T) ( = DSM 24185(T)  = VKM B-2672(T)).